Using the BioMark system requires some additional processing over traditional RT-PCR. Using only 10nL in each reaction, ensuring that each reaction has sufficient template is a primary concern. To create a concentrated enough template, the BioMark system requires a pre-amplification where all of the primer pairs to be tested are mixed together with each sample and amplified by standard PCR. This increases the concentration of the specific product enough to ensure that sufficient template is added to each of the final reactions.

Using the BioMark system requires some additional processing over traditional RT-PCR. Using only 10nL in each reaction, ensuring that each reaction has sufficient template is a primary concern. To create a concentrated enough template, the BioMark system requires a pre-amplification where all of the primer pairs to be tested are mixed together with each sample and amplified by standard PCR. This increases the concentration of the specific product enough to ensure that sufficient template is added to each of the final reactions.

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* <B>[[BioMicroCenter:Fluid_CAL| Schedule time on the Biomark]]</B><BR><BR>

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* <B>[https://mit-ki.ilabsolutions.com/equipment/show/261686/?tab=schedule Schedule time on the Biomark]</B><BR><BR>

Use of the BioMark costs '''$150''' per use to help defray the service contract charge.

Use of the BioMark costs '''$150''' per use to help defray the service contract charge.

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== Traditional Real Time PCR ==

== Traditional Real Time PCR ==

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[[Image:Opticon2_system.gif|right]]

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===MJ Research Real Time PCR Machine===

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The MJ Research PCR Machine enables multicolor capability allowing detection of SYBR® Green I or FAM in the first channel, and a range of fluorophores in the second channel — including TET, HEX, VIC, and TAMRA — for a multitude of applications such as RT-qPCR and allelic discrimination. The DNA Engine® thermal cycler offers precision thermal control and a temperature gradient feature permits simultaneous incubation at 12 different temperatures to optimize reactions in a single run. The real-time results allow for plotting of signal intensity vs. cycle number and graphically monitoring the thermal profile during the run. The extraordinary sensitivity permits reliable detection of one initial template copy, while delivering a linear range of up to ten orders of magnitude in starting copy number (with appropriate chemistry). Users are currently charged '''$10''' per plate for the use of this machine. <BR>

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* <B>[[BioMicroCenter:MJO_CAL|Schedule Time on the MJ Opticon]]</B><BR><BR>

[[Image:LC480.jpg|right]]

[[Image:LC480.jpg|right]]

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The [https://www.roche-applied-science.com/sis/rtpcr/htc/index.jsp LightCycler 480 Real-Time PCR System] is a fully integrated multiwell-plate based real-time PCR platform for highly accurate qualitative and quantitative detection of nucleic acids. Building on the benefits of Roche's capillary-based LightCycler® Systems, it goes one step further in offering enhanced throughput, compatibility with automation equipment and maximum flexibility regarding hard- and software. Providing novel ways to combine speed and accuracy without compromises, the LightCycler® 480 Real-Time PCR System meets the needs of a broad range of applications in research fields such as gene expression studies, discovery and analysis of genetic variation or array data validation.

The [https://www.roche-applied-science.com/sis/rtpcr/htc/index.jsp LightCycler 480 Real-Time PCR System] is a fully integrated multiwell-plate based real-time PCR platform for highly accurate qualitative and quantitative detection of nucleic acids. Building on the benefits of Roche's capillary-based LightCycler® Systems, it goes one step further in offering enhanced throughput, compatibility with automation equipment and maximum flexibility regarding hard- and software. Providing novel ways to combine speed and accuracy without compromises, the LightCycler® 480 Real-Time PCR System meets the needs of a broad range of applications in research fields such as gene expression studies, discovery and analysis of genetic variation or array data validation.

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There is a '''$10''' charge per plate will be implemented to cover the cost of the service contract. The LightCycler 480 is only available for use by MIT [[BioMicroCenter:CoreDeps|Core departments]].

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There is a charge per plate to cover the cost of the service contract.

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96 well plates ($6 per plate) and SYBR Green ($40 per mL) can also be supplied on demand for use on the LightCycler480

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96 well plates and SYBR Green can also be supplied on demand for use on the LightCycler480

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'''Please Note:''' There are three LightCycler systems (Thing 1, Thing 2, and Thing 3) that have a sign up maximum of four hours per day during business hours (10AM to 5PM), all time slots are available the night before even if it exceeds the maximum. New users who wished to be trained must be [[BioMicroCenter:CoreDeps|Core Lab members]].

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'''Please Note:''' There are three LightCycler systems (Thing 1, Thing 2, and Thing 3) that have a sign up maximum of four hours per day during business hours (10AM to 5PM), all time slots are available the night before even if it exceeds the maximum.

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[http://www.google.com/calendar Schedule Time on the LightCycler 480]

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[https://mit-ki.ilabsolutions.com/equipment/show/261680/?tab=schedule Schedule Time on the LightCycler 480]

The Fluidigm BioMark system is a highly parallelized system allowing for running thousands of RT-PCR reactions on a single cartridge. Useful for genotyping, gene expression analysis and digital PCR, the BioMark cassette works using thousands of NanoFlex(TM) valves to fill thousands of individual reactions from a matrix of samples and primers. Standard Geneotyping / Gene Expression cassettes come in 48x48 and 96x96 format allowing either ~2,500 or ~10,000 reactions on a single cassette. RT-PCR in the BioMark system is compatible with TaqMan(TM), the Roche Universal priming kit, and SYBR Green technologies.

Using the BioMark system requires some additional processing over traditional RT-PCR. Using only 10nL in each reaction, ensuring that each reaction has sufficient template is a primary concern. To create a concentrated enough template, the BioMark system requires a pre-amplification where all of the primer pairs to be tested are mixed together with each sample and amplified by standard PCR. This increases the concentration of the specific product enough to ensure that sufficient template is added to each of the final reactions.

Use of the BioMark costs $150 per use to help defray the service contract charge.
For training please email biomicro@mit.edu

Traditional Real Time PCR

Light Cycler 480 II Real-time PCR Machines

The LightCycler 480 Real-Time PCR System is a fully integrated multiwell-plate based real-time PCR platform for highly accurate qualitative and quantitative detection of nucleic acids. Building on the benefits of Roche's capillary-based LightCycler® Systems, it goes one step further in offering enhanced throughput, compatibility with automation equipment and maximum flexibility regarding hard- and software. Providing novel ways to combine speed and accuracy without compromises, the LightCycler® 480 Real-Time PCR System meets the needs of a broad range of applications in research fields such as gene expression studies, discovery and analysis of genetic variation or array data validation.

There is a charge per plate to cover the cost of the service contract.

96 well plates and SYBR Green can also be supplied on demand for use on the LightCycler480

Please Note: There are three LightCycler systems (Thing 1, Thing 2, and Thing 3) that have a sign up maximum of four hours per day during business hours (10AM to 5PM), all time slots are available the night before even if it exceeds the maximum.